Scalable Bayesian divergence time estimation with ratio transformations

This repository contains the instructions and files to reproduce the analyses performed in the "Scalable Bayesian divergence time estimation with ratio transformations" paper by Ji et al.

We provide two ways for users to setup software to reproduce our results. Please kindly refer to the section Docker image if you'd like to run BEAST within docker container which is local and should not disturb your other BEAST installations. Please kindly refer to the section Global installation if you'd like to install BEAST and BEAGLE gloably which could potentially interfere with your other BEAST installations. You could find a separate Reproducing the analyses section under each installation method to follow.

Docker image

We provide a docker image to streamline software setup. To build the docker image for x86_64 systems (e.g. Intel/AMD chips), please run

cd where_this_repository_is_stored
docker build --platform x86_64 -t beast docker

To build the docker image for arm_64 systems (e.g. Apple silicon chips), please run

cd where_this_repository_is_stored
docker build --platform ARM64 -t beast docker

Reproducing the analyses

You may use the following commands for each case of the three data sets as described in the manuscript.

Let's open an interactive bash session under docker container.

docker run --mount type=bind,src="$(pwd)",target=/tmp -it beast bash

To run each of the analysis, please use the corresponding command below in the interactive bash shell.

West Nile Virus

"time" scenario

HMC

 beast -load_state xmls/WNV/WNV_skyline_onlyHeights_HMC_save -overwrite xmls/WNV/WNV_Skyline_onlyHeights_HMC.xml

Univariable

 beast -load_state xmls/WNV/WNV_skyline_onlyHeights_Serial_save -overwrite xmls/WNV/WNV_skyline_onlyHeight_Univariable.xml

"rate & time" scenario

HMC

 beast -load_state xmls/WNV/WNV_skyline_rateNTime_HMC_save -overwrite xmls/WNV/WNV_Skyline_rateNTime_only_HMC.xml

Univariable

 beast -load_state xmls/WNV/WNV_skyline_rateNTime_Serial_save -overwrite xmls/WNV/WNV_skyline_rateNTime_Univariable.xml

Rabies virus

"time" scenario

HMC

 beast -load_state xmls/RRV/RABV_Exp_onlyHeights_HMC_save -overwrite xmls/RRV/RacRABV_Exp_onlyHeights_HMC.xml

Univariable

 beast -load_state xmls/RRV/RABV_Exp_onlyHeights_Univariable_save -overwrite xmls/RRV/RacRABV_Exp_onlyHeights_Univariable.xml

"rate & time" scenario

HMC

 beast -load_state xmls/RRV/RABV_Exp_HMC_rateNtime_save -overwrite xmls/RRV/RacRABV_Exp_rateNTime_HMC.xml

Univariable

 beast -load_state xmls/RRV/RABV_Exp_rateNTime_Univariable_save -overwrite xmls/RRV/RacRABV_Exp_rateNTime_Univariable.xml

Lassa Virus

"time" scenario

HMC

 beast -load_state xmls/Lassa/Lassa_skygrid_onlyHeights_HMC_save -overwrite xmls/Lassa/Lassa_S_skygrid_onlyHeights_HMC.xml

Univariable

 beast -load_state xmls/Lassa/Lassa_skygrid_onlyHeights_Univariable_save -overwrite xmls/Lassa/Lassa_S_skygrid_onlyHeights_Univariable.xml

"rate & time" scenario

HMC

 beast -load_state xmls/Lassa/Lassa_skygrid_rateNTime_HMC_save -overwrite xmls/Lassa/Lassa_S_skygrid_rateNTime_HMC.xml

Univariable

 beast -load_state xmls/Lassa/Lassa_skygrid_rateNTime_Univariable_save -overwrite xmls/Lassa/Lassa_S_skygrid_rateNTime_Univariable.xml

Ebola Virus

HMC

	beast -seed 666 -overwrite xmls/EVD/ebov_HMC_all.xml

Algae

"time" scenario

HMC

 beast -load_state xmls/Algae/algae_hmc_onlyHeight_save -overwrite xmls/Algae/Algae_HMC_onlyHeight.xml

Univariable

 beast -load_state xmls/Algae/algae_univariate_onlyHeight_save -overwrite xmls/Algae/Algae_univariate_onlyHeight.xml

"rate & time" scenario

HMC

 beast -load_state xmls/Algae/algae_hmc_rateNTime_save -overwrite xmls/Algae/Algae_HMC_rateNTime.xml

Univariable

 beast -load_state xmls/Algae/algae_univariate_rateNTime_save -overwrite xmls/Algae/Algae_univariate_rateNTime.xml

Global installations

####Setting up BEAGLE Please follow the BEAGLE installation instructions. But get the hmc-clock branch.

For Mac users, the following commands will compile the CPU version of BEAGLE. Follow the instructions if you need to install any other dependent software.

xcode-select --install
brew install libtool autoconf automake
git clone -b hmc-clock https://github.com/beagle-dev/beagle-lib.git
git checkout 3bdb30bd645e15983f8c8cf952564813e306ad83
cd beagle-lib
mkdir build
cd build
cmake -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF ..
sudo make install

For Linux users, the commands are similar.

sudo apt-get install build-essential autoconf automake libtool git pkg-config openjdk-9-jdk
git clone -b hmc-clock https://github.com/beagle-dev/beagle-lib.git
git checkout 3bdb30bd645e15983f8c8cf952564813e306ad83
cd beagle-lib
mkdir build
cd build
cmake -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF ..
sudo make install

The libraries are installed into /usr/local/lib. You can find them by ls /usr/local/lib/*beagle*.

Setting up BEAST

The following commands will compile the hmc-clock branch of BEAST.

git clone -b hmc-clock https://github.com/beast-dev/beast-mcmc.git
cd beast-mcmc
git checkout 17da204e2d9bdadb6c8284fd092413054f161bdc
ant

For Mac users, you may need to install ant by brew install ant through Homebrew.

For Linux users, you can install ant by sudo apt-get install ant.

This will compile the jar files under beast-mcmc/build/dist/ where you can find beast.jar, beauti.jar and trace.jar.

Reproducing the analyses

You may use the following commands for each case of the three data sets as described in the manuscript.

Change your working directory to where you want to store the resulting log files first.

cd where_you_want_to_save_results

West Nile Virus

"time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_Skyline_onlyHeights_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeights_Serial_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeight_Univariable.xml

"rate & time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_HMC_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_Skyline_rateNTime_only_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_Serial_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_Univariable.xml

Rabies virus

"time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_onlyHeights_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_onlyHeights_Univariable_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_onlyHeights_Univariable.xml

"rate & time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_HMC_rateNtime_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_rateNTime_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_rateNTime_Univariable_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_rateNTime_Univariable.xml

Lassa Virus

"time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_onlyHeights_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_onlyHeights_Univariable_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_onlyHeights_Univariable.xml

"rate & time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_rateNTime_HMC_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_rateNTime_HMC.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_rateNTime_Univariable_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_rateNTime_Univariable.xml

Ebola Virus

HMC

	java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -seed 666 -overwrite where_this_repository_is_stored/xmls/EVD/ebov_HMC_all.xml

Algae

"time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Algae/algae_hmc_onlyHeight_save -overwrite where_this_repository_is_stored/xmls/Algae/Algae_HMC_onlyHeight.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Algae/algae_univariate_onlyHeight_save -overwrite where_this_repository_is_stored/xmls/Algae/Algae_univariate_onlyHeight.xml

"rate & time" scenario

HMC

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Algae/algae_hmc_rateNTime_save -overwrite where_this_repository_is_stored/xmls/Algae/Algae_HMC_rateNTime.xml

Univariable

 java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Algae/algae_univariate_rateNTime_save -overwrite where_this_repository_is_stored/xmls/Algae/Algae_univariate_rateNTime.xml

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Scalable Bayesian divergence time estimation with ratio transformations

Docker image

Reproducing the analyses

West Nile Virus

Rabies virus

Lassa Virus

Ebola Virus

Algae

Global installations

Setting up BEAST

Reproducing the analyses

West Nile Virus

Rabies virus

Lassa Virus

Ebola Virus

Algae

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Scalable Bayesian divergence time estimation with ratio transformations

Docker image

Reproducing the analyses

West Nile Virus

Rabies virus

Lassa Virus

Ebola Virus

Algae

Global installations

Setting up BEAST

Reproducing the analyses

West Nile Virus

Rabies virus

Lassa Virus

Ebola Virus

Algae

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